Microbial Processes in the Vadose Zone

Holden, Patricia A.; Fierer, Noah

doi:10.2136/vzj2005.0001

Cited by 113 publications

(47 citation statements)

References 165 publications

(409 reference statements)

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“…The non-obvious implication arises from the fact that the soil water retention curve reflects the cumulative pore size distribution of the soil (Jury and Horton, 2004) and the actual soil moisture reflects water that is stored among different size fractions of the wetted pore space.…”

Section: Theory and Model Implementationmentioning

confidence: 99%

“…Crucially, soil moisture crucially controls CO 2 emissions of forest soils (Koehler et al, 2010) denitrification and related trace gas emissions into the atmosphere (Koehler et al, 2012) as well as metabolic transformations of pesticides (e.g. Holden and Fierer, 2005). Nonetheless, soil moisture controls splitting of rainfall into surface runoff and (preferential) infiltration Lee et al, 2007;Loos and Elsenbeer, 2011;Bronstert et al, 2012;Zimmermann et al, 2013;Klaus et al, 2014).…”

Section: Introductionmentioning

confidence: 99%

“…Water storage in the unsaturated zone is controlled by capillary forces which increase non-linearly with decreasing pore size, because water acts as a wetting fluid in soil (Jury and Horton, 2004). The standard approach to represent capillary-and gravity-controlled soil water dynamics is the Darcy-Richards equation in combination with suitable soil water characteristics.…”

Section: Introductionmentioning

confidence: 99%

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A Lagrangian model for soil water dynamics during rainfall-driven conditions

Zehe

Jackisch

2016

Hydrol. Earth Syst. Sci.

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Abstract. Within this study we propose a stochastic approach to simulate soil water dynamics in the unsaturated zone by using a non-linear, space domain random walk of water particles. Soil water is represented by particles of constant mass, which travel according to the Itô form of the Fokker-Planck equation. The model concept builds on established soil physics by estimating the drift velocity and the diffusion term based on the soil water characteristics. A naive random walk, which assumes all water particles to move at the same drift velocity and diffusivity, overestimated depletion of soil moisture gradients compared to a Richards solver. This is because soil water and hence the corresponding water particles in smaller pore size fractions are, due to the non-linear decrease in soil hydraulic conductivity with decreasing soil moisture, much less mobile. After accounting for this subscale variability in particle mobility, the particle model and a Richards solver performed highly similarly during simulated wetting and drying circles in three distinctly different soils. Both models were in very good accordance during rainfall-driven conditions, regardless of the intensity and type of the rainfall forcing and the shape of the initial state. Within subsequent drying cycles the particle model was typically slightly slower in depleting soil moisture gradients than the Richards model.Within a real-world benchmark, the particle model and the Richards solver showed the same deficiencies in matching observed reactions of topsoil moisture to a natural rainfall event. The particle model performance, however, clearly improved after a straightforward implementation of rapid nonequilibrium infiltration, which treats event water as different types of particles, which travel initially in the largest pore fraction at maximum velocity and experience a slow diffusive mixing with the pre-event water particles. The proposed Lagrangian approach is hence a promising, easy-to-implement alternative to the Richards equation for simulating rainfalldriven soil moisture dynamics, which offers straightforward opportunities to account for preferential, non-equilibrium flow.

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Section: Theory and Model Implementationmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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A Lagrangian model for soil water dynamics during rainfall-driven conditions

Zehe

Jackisch

2016

Hydrol. Earth Syst. Sci.

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“…In contrast aerobic motile bacteria can even move into the top zone of the capillary fringe (CF, spanning from the groundwater table to still visible moisture above it in a quartz sand aquifer) above the water-saturated zone of quartz sand and form a dense biofilm in the still highly saturated interface region of the CF [31]. Biofilm formation in a substrate-limited, watersaturated underground and in the CF is however a very slow process due to severe nutrient limitation in this often still pristine oligotrophic environment [18], [19], [20] and [25]. Single aspects of biofilm formation have been reviewed previously by [43], covering among others the changes of the "morphological structure of the extracellular polymeric substances (EPS) matrix under varying hydration states, its role in maintenance of aquatic microhabitats and facilitating nutrient diffusion under desiccated conditions, and potential modification of macroscopic hydrologic properties of host porous media".…”

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confidence: 99%

Influence of Increasing Concentrations of Organic Pollutants on Biofilm Formation and Flow Parameters in a Sand-aquifer and Its Capillary Fringe.

Jost¹,

Winter²,

Gallert³

2017

EPP

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Abstract. We followed the development of a Pseudomonas fluorescens biofilm on quartz sand in an instrumented horizontal flow-through stainless steel container (SSC) in lysimeter-scale, to investigate its impact on physical soil parameters within the aquifer and the capillary fringe (CF). Increasingly concentrated biodegradable substances in a liquid medium were pumped through the sand in the SSC creating an artificial aquifer. Biofilm development and its influence on flow parameters and oxygen concentration profiles, as well as temperature or water suction changes with time were determined. After more than 19 weeks of medium flow, at DOC concentrations of finally about 300 mg/L, P. fluorescens formed a strong biofilm and the highest biomass concentrations with up to 2.8 mg volatile solids per g dry sand were found in the transition zone of the CF. The soil temperature, which was slightly increased, or the water suction was significantly influenced during the experiment. The effects were strongest within the first 0.3 m of flow stretch, where the highest biomass values were detected. During the total experimental duration of 54 weeks the average flow velocity was reduced by up to 15 % due to clogging effects and the oxygen profiles were changed drastically. Results may be representative for real polluted aquifers. Keywords:Pseudomonas fluorescens, sand aquifer, capillary fringe, soil contamination, biofilm formation, biological clogging. IntroductionSoil and groundwater are naturally inhabited by a vast variety of prokaryotes. It was estimated that 2.5 x 10 29 microorganisms live in the top 8 m of the terrestrial subsurface and at least 2.5 x 10 30 microorganisms below 8 m depth, either suspended in the water phase or attached onto organic and mineral compounds of top soil and the underground [53]. Anaerobic bacteria in deep soil layers may ferment organic pollutants to mainly fatty acids whereas aerobic bacteria in upper soil layers may respire organic pollutants in the presence of oxygen to carbon dioxide and thus contribute to "clean-up". There seems to be a spatial heterogeneity of microorganisms. Whereas mainly aerobic bacteria, fungi and protozoa colonize soil surface layers, the proportion of mainly anaerobic bacteria (most of them are "fermenters") and of Actinomycetes increases with depth in the underground in the vicinity and below the groundwater table. These population changes are accompanied by a significantly decreasing diversity of microorganisms [17] and by a decrease of physiological functions [45]. Groundwater bacteria tend to form a biofilm on mineral surfaces of soil particles and may cause preferential flow paths or clogging in heterogeneous soil compartments [45]. In contrast aerobic motile bacteria can even move into the top zone of the capillary fringe (CF, spanning from the groundwater table to still visible moisture above it in a quartz sand aquifer) above the water-saturated zone of quartz sand and form a dense biofilm in the still highly saturated interface region of the CF [31]. Biofi...

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“…Changes in microbial community structure with soil depth have been attributed to the microbial response to contrasting physical and chemical conditions associated with surface, vadose zone, and saturated soils (Holden and Fierer, 2005). Environmental factors that influence microbial community composition and diversity include (but are not limited to) pH (Eichorst et al, 2007), particle size (Sessitsch et al, 2001), organic carbon content (Zhou et al, 2002), nutrient availability (Fierer et al, 2003a), water content (Treves et al, 2003), and oxygen concentration (Van Der Heijden et al, 2008).…”

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confidence: 99%